Does the same Groove Template work if you try to MIDI regions? Is Q-strength set to 100%? Which value do you have for Q-range?
Are you sure that there are notes throughout the source region (the one you made into a Groove template)- including in at the beginning of that region?

Logician

You have to have transients in the audio that are appropriately located to be quantized. For example, you may think you are working with 16ths, but the groove may be a half time feel and everything is 1/8ths. So applying a 16th shuffle feel will get you nowhere.

Can you quantize the flexed audio file to an extreme (and obvious) quantize value, like 1/4? At least you'd know the region can or cannot be quantized. Speaking of region, you can enable/disable flex on a per region basis - the check box is in the inspector. Make sure this is checked.....